library(multiMiR)
## Welcome to multiMiR.
## 
## multiMiR database URL has been set to the 
## default value: http://multimir.org/
## 
## Database Version: 2.3.0  Updated: 2020-04-15
library(clusterProfiler)
## 
## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
## 
## Please cite:
## 
## S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang, Q Wang, B Liu, R Wang,
## W Xie, T Wu, L Xie, G Yu. Using clusterProfiler to characterize
## multiomics data. Nature Protocols. 2024, doi:10.1038/s41596-024-01020-z
## 
## Attaching package: 'clusterProfiler'
## The following object is masked from 'package:multiMiR':
## 
##     select
## The following object is masked from 'package:stats':
## 
##     filter
library(org.Hs.eg.db)
## Loading required package: AnnotationDbi
## Loading required package: stats4
## Loading required package: BiocGenerics
## 
## Attaching package: 'BiocGenerics'
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##     IQR, mad, sd, var, xtabs
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##     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
##     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
##     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
##     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
##     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
##     tapply, union, unique, unsplit, which.max, which.min
## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## Loading required package: IRanges
## Loading required package: S4Vectors
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## Attaching package: 'S4Vectors'
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## Attaching package: 'AnnotationDbi'
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##     select
## 
library(stringr)
library(ggplot2)

0. Loading of Results

A. List of all Gene names in the dataset

gene.names = readRDS("data/derived/unique_gene_names.rds")

B. Selected Features

results.squeezy = readRDS("data/sel_features/results_squeezy_coef.rds")
sel.features = results.squeezy
sel.features
## $fold3
## $fold3$elasticnet_0.5
## $fold3$elasticnet_0.5$multigroup
##    FN1.R2Gn   G6PD.RPPA   FASN.RPPA   MSH6.RPPA   TFRC.RPPA 
## -0.05082038  1.79344129  1.83979725  0.52730351  0.15202426 
## 
## $fold3$elasticnet_0.5$onegroup
##    FN1.R2Gn   G6PD.RPPA   FASN.RPPA  PDCD4.RPPA   MSH6.RPPA   TFRC.RPPA 
## -0.05082038  1.79344129  1.83979725  1.78890341  0.52730351  0.15202426 
## 
## 
## $fold3$lasso
## $fold3$lasso$multigroup
##    FN1.R2Gn   G6PD.RPPA   FASN.RPPA   TFRC.RPPA 
## -0.05082038  1.79344129  1.83979725  0.15202426 
## 
## $fold3$lasso$onegroup
## FASN.RPPA TFRC.RPPA 
## 1.8397972 0.1520243 
## 
## 
## 
## $fold5
## $fold5$elasticnet_0.5
## $fold5$elasticnet_0.5$multigroup
##    FN1.R2Gn   G6PD.RPPA   FASN.RPPA   MSH6.RPPA   TFRC.RPPA 
## -0.05082038  1.79344129  1.83979725  0.52730351  0.15202426 
## 
## $fold5$elasticnet_0.5$onegroup
##    FN1.R2Gn   G6PD.RPPA   FASN.RPPA  PDCD4.RPPA   MSH6.RPPA   TFRC.RPPA 
## -0.05082038  1.79344129  1.83979725  1.78890341  0.52730351  0.15202426 
## 
## 
## $fold5$lasso
## $fold5$lasso$multigroup
##    FN1.R2Gn   G6PD.RPPA   FASN.RPPA   TFRC.RPPA 
## -0.05082038  1.79344129  1.83979725  0.15202426 
## 
## $fold5$lasso$onegroup
## FASN.RPPA TFRC.RPPA 
## 1.8397972 0.1520243 
## 
## 
## 
## $fold10
## $fold10$elasticnet_0.5
## $fold10$elasticnet_0.5$multigroup
##    FN1.R2Gn   G6PD.RPPA   FASN.RPPA   MSH6.RPPA   TFRC.RPPA 
## -0.05082038  1.79344129  1.83979725  0.52730351  0.15202426 
## 
## $fold10$elasticnet_0.5$onegroup
##    FN1.R2Gn   G6PD.RPPA   FASN.RPPA  PDCD4.RPPA   MSH6.RPPA   TFRC.RPPA 
## -0.05082038  1.79344129  1.83979725  1.78890341  0.52730351  0.15202426 
## 
## 
## $fold10$lasso
## $fold10$lasso$multigroup
##    FN1.R2Gn   G6PD.RPPA   FASN.RPPA   TFRC.RPPA 
## -0.05082038  1.79344129  1.83979725  0.15202426 
## 
## $fold10$lasso$onegroup
## FASN.RPPA TFRC.RPPA 
## 1.8397972 0.1520243

1. Convert microRNA to genes

Also remove the ending “.R2Gn” and “.RPPA” from gene names.

split.by.omic = function(variable.list) {
  out.mRSG = variable.list[startsWith(variable.list, "hsa")]
  out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
  out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
  out = list("miRNASeqGene" = out.mRSG,
             "RNASeq2GeneNorm" = out.R2Gn,
             "RPPAArray" = out.RPPA)
  out
}
multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
  multiomics.list = split.by.omic(sel.features)
  # Convert miRNASeqGene to target GENE names
  # Skipped and returns an empty list instead of the list of select features,
  # or if microRNA features are explicitly dropped (drop.miRNA = T).
  # (Usually done when the features has only a few miRNA and unable to target any genes)
  if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
    if (!full.search) { # Search only among the 198 genes in ACC, recommended
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          target = gene.names,
                          table = table,
                          summary = T)
    mRSG.target.genes = unique(targets@data$target_symbol)
    } else { # Search the full dataset, not recommended. 
             # Use only if ACC gene search returns nothing or fails.
             # Genes not in the ACC genes need to be manually removed.
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          table = table,
                          summary = T)  
    mRSG.target.genes = unique(targets@data$target_symbol)
    }
    
  } else {
    mRSG.target.genes = list()
  }
  #Remove suffix for Pathway Analysis Compatibility
  R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
  
  RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
  
  #Join all cleaned-up genes are remove duplicates.
  out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes)
  out = as.character(unique(out1))
  out
}
geneNames <- list("3F_0.5_Multi"=multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$multigroup)),
                  "3F_0.5_One"=multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$onegroup)),
                  "3F_1_Multi"=multiomics.to.GENES(names(sel.features$fold3$lasso$multigroup)),
                  "3F_1_One"=multiomics.to.GENES(names(sel.features$fold3$lasso$multigroup)),
                  
                  # 5-Fold and 10-Fold CV results are exactly the same as 3-Fold,
                  # They are kept here for completeness.
                  "5F_0.5_Multi"=multiomics.to.GENES(names(sel.features$fold5$elasticnet_0.5$multigroup)),
                  "5F_0.5_One"=multiomics.to.GENES(names(sel.features$fold5$elasticnet_0.5$onegroup)),
                  "5F_1_Multi"=multiomics.to.GENES(names(sel.features$fold5$lasso$multigroup)),
                  "5F_1_One"=multiomics.to.GENES(names(sel.features$fold5$lasso$multigroup)),
                  
                  "10F_0.5_Multi"=multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.5$multigroup)),
                  "10F_0.5_One"=multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.5$onegroup)),
                  "10F_1_Multi"=multiomics.to.GENES(names(sel.features$fold10$lasso$multigroup)),
                  "10F_1_One"=multiomics.to.GENES(names(sel.features$fold10$lasso$multigroup))
                  )
geneNames
## $`3F_0.5_Multi`
## [1] "FN1"  "G6PD" "FASN" "MSH6" "TFRC"
## 
## $`3F_0.5_One`
## [1] "FN1"   "G6PD"  "FASN"  "PDCD4" "MSH6"  "TFRC" 
## 
## $`3F_1_Multi`
## [1] "FN1"  "G6PD" "FASN" "TFRC"
## 
## $`3F_1_One`
## [1] "FN1"  "G6PD" "FASN" "TFRC"
## 
## $`5F_0.5_Multi`
## [1] "FN1"  "G6PD" "FASN" "MSH6" "TFRC"
## 
## $`5F_0.5_One`
## [1] "FN1"   "G6PD"  "FASN"  "PDCD4" "MSH6"  "TFRC" 
## 
## $`5F_1_Multi`
## [1] "FN1"  "G6PD" "FASN" "TFRC"
## 
## $`5F_1_One`
## [1] "FN1"  "G6PD" "FASN" "TFRC"
## 
## $`10F_0.5_Multi`
## [1] "FN1"  "G6PD" "FASN" "MSH6" "TFRC"
## 
## $`10F_0.5_One`
## [1] "FN1"   "G6PD"  "FASN"  "PDCD4" "MSH6"  "TFRC" 
## 
## $`10F_1_Multi`
## [1] "FN1"  "G6PD" "FASN" "TFRC"
## 
## $`10F_1_One`
## [1] "FN1"  "G6PD" "FASN" "TFRC"
saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_squeezy.rds")

2. Pathway Analysis

A. GO Classification

groupGO does not work with Squeey results, as there are too few genes (<=6) selected.

ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]

  ggo_MF[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="MF",
    keyType="SYMBOL",
    readable=TRUE)
  
  ggo_BP[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="BP",
    keyType="SYMBOL",
    readable=TRUE)

  ggo_CC[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="CC",
    keyType="SYMBOL",
    readable=TRUE)    
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
for(z in 1:length(geneNames)) {
  print(head(ggo_MF[[z]]))
  print(head(ggo_BP[[z]]))
  print(head(ggo_CC[[z]]))
}
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/5
## GO:0003824 GO:0003824           catalytic activity     3       3/5
## GO:0005198 GO:0005198 structural molecule activity     1       1/5
## GO:0005215 GO:0005215         transporter activity     0       0/5
## GO:0005488 GO:0005488                      binding     5       5/5
## GO:0009055 GO:0009055   electron transfer activity     0       0/5
##                             geneID
## GO:0003774                        
## GO:0003824          G6PD/FASN/MSH6
## GO:0005198                     FN1
## GO:0005215                        
## GO:0005488 FN1/G6PD/FASN/MSH6/TFRC
## GO:0009055                        
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     1       1/5
## GO:0002376 GO:0002376 immune system process     4       4/5
## GO:0008152 GO:0008152     metabolic process     5       5/5
## GO:0009987 GO:0009987      cellular process     5       5/5
## GO:0016032 GO:0016032         viral process     1       1/5
## GO:0022414 GO:0022414  reproductive process     1       1/5
##                             geneID
## GO:0000003                    MSH6
## GO:0002376      FN1/G6PD/MSH6/TFRC
## GO:0008152 FN1/G6PD/FASN/MSH6/TFRC
## GO:0009987 FN1/G6PD/FASN/MSH6/TFRC
## GO:0016032                    TFRC
## GO:0022414                    MSH6
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     3       3/5
## GO:0044423 GO:0044423           virion component     0       0/5
## GO:0110165 GO:0110165 cellular anatomical entity     5       5/5
##                             geneID
## GO:0032991           FN1/MSH6/TFRC
## GO:0044423                        
## GO:0110165 FN1/G6PD/FASN/MSH6/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/6
## GO:0003824 GO:0003824           catalytic activity     3       3/6
## GO:0005198 GO:0005198 structural molecule activity     1       1/6
## GO:0005215 GO:0005215         transporter activity     0       0/6
## GO:0005488 GO:0005488                      binding     6       6/6
## GO:0009055 GO:0009055   electron transfer activity     0       0/6
##                                   geneID
## GO:0003774                              
## GO:0003824                G6PD/FASN/MSH6
## GO:0005198                           FN1
## GO:0005215                              
## GO:0005488 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0009055                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     1       1/6
## GO:0002376 GO:0002376 immune system process     4       4/6
## GO:0008152 GO:0008152     metabolic process     6       6/6
## GO:0009987 GO:0009987      cellular process     6       6/6
## GO:0016032 GO:0016032         viral process     1       1/6
## GO:0022414 GO:0022414  reproductive process     1       1/6
##                                   geneID
## GO:0000003                          MSH6
## GO:0002376            FN1/G6PD/MSH6/TFRC
## GO:0008152 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0009987 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0016032                          TFRC
## GO:0022414                          MSH6
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     3       3/6
## GO:0044423 GO:0044423           virion component     0       0/6
## GO:0110165 GO:0110165 cellular anatomical entity     6       6/6
##                                   geneID
## GO:0032991                 FN1/MSH6/TFRC
## GO:0044423                              
## GO:0110165 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/4
## GO:0003824 GO:0003824           catalytic activity     2       2/4
## GO:0005198 GO:0005198 structural molecule activity     1       1/4
## GO:0005215 GO:0005215         transporter activity     0       0/4
## GO:0005488 GO:0005488                      binding     4       4/4
## GO:0009055 GO:0009055   electron transfer activity     0       0/4
##                        geneID
## GO:0003774                   
## GO:0003824          G6PD/FASN
## GO:0005198                FN1
## GO:0005215                   
## GO:0005488 FN1/G6PD/FASN/TFRC
## GO:0009055                   
##                    ID           Description Count GeneRatio             geneID
## GO:0000003 GO:0000003          reproduction     0       0/4                   
## GO:0002376 GO:0002376 immune system process     3       3/4      FN1/G6PD/TFRC
## GO:0008152 GO:0008152     metabolic process     4       4/4 FN1/G6PD/FASN/TFRC
## GO:0009987 GO:0009987      cellular process     4       4/4 FN1/G6PD/FASN/TFRC
## GO:0016032 GO:0016032         viral process     1       1/4               TFRC
## GO:0022414 GO:0022414  reproductive process     0       0/4                   
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     2       2/4
## GO:0044423 GO:0044423           virion component     0       0/4
## GO:0110165 GO:0110165 cellular anatomical entity     4       4/4
##                        geneID
## GO:0032991           FN1/TFRC
## GO:0044423                   
## GO:0110165 FN1/G6PD/FASN/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/4
## GO:0003824 GO:0003824           catalytic activity     2       2/4
## GO:0005198 GO:0005198 structural molecule activity     1       1/4
## GO:0005215 GO:0005215         transporter activity     0       0/4
## GO:0005488 GO:0005488                      binding     4       4/4
## GO:0009055 GO:0009055   electron transfer activity     0       0/4
##                        geneID
## GO:0003774                   
## GO:0003824          G6PD/FASN
## GO:0005198                FN1
## GO:0005215                   
## GO:0005488 FN1/G6PD/FASN/TFRC
## GO:0009055                   
##                    ID           Description Count GeneRatio             geneID
## GO:0000003 GO:0000003          reproduction     0       0/4                   
## GO:0002376 GO:0002376 immune system process     3       3/4      FN1/G6PD/TFRC
## GO:0008152 GO:0008152     metabolic process     4       4/4 FN1/G6PD/FASN/TFRC
## GO:0009987 GO:0009987      cellular process     4       4/4 FN1/G6PD/FASN/TFRC
## GO:0016032 GO:0016032         viral process     1       1/4               TFRC
## GO:0022414 GO:0022414  reproductive process     0       0/4                   
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     2       2/4
## GO:0044423 GO:0044423           virion component     0       0/4
## GO:0110165 GO:0110165 cellular anatomical entity     4       4/4
##                        geneID
## GO:0032991           FN1/TFRC
## GO:0044423                   
## GO:0110165 FN1/G6PD/FASN/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/5
## GO:0003824 GO:0003824           catalytic activity     3       3/5
## GO:0005198 GO:0005198 structural molecule activity     1       1/5
## GO:0005215 GO:0005215         transporter activity     0       0/5
## GO:0005488 GO:0005488                      binding     5       5/5
## GO:0009055 GO:0009055   electron transfer activity     0       0/5
##                             geneID
## GO:0003774                        
## GO:0003824          G6PD/FASN/MSH6
## GO:0005198                     FN1
## GO:0005215                        
## GO:0005488 FN1/G6PD/FASN/MSH6/TFRC
## GO:0009055                        
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     1       1/5
## GO:0002376 GO:0002376 immune system process     4       4/5
## GO:0008152 GO:0008152     metabolic process     5       5/5
## GO:0009987 GO:0009987      cellular process     5       5/5
## GO:0016032 GO:0016032         viral process     1       1/5
## GO:0022414 GO:0022414  reproductive process     1       1/5
##                             geneID
## GO:0000003                    MSH6
## GO:0002376      FN1/G6PD/MSH6/TFRC
## GO:0008152 FN1/G6PD/FASN/MSH6/TFRC
## GO:0009987 FN1/G6PD/FASN/MSH6/TFRC
## GO:0016032                    TFRC
## GO:0022414                    MSH6
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     3       3/5
## GO:0044423 GO:0044423           virion component     0       0/5
## GO:0110165 GO:0110165 cellular anatomical entity     5       5/5
##                             geneID
## GO:0032991           FN1/MSH6/TFRC
## GO:0044423                        
## GO:0110165 FN1/G6PD/FASN/MSH6/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/6
## GO:0003824 GO:0003824           catalytic activity     3       3/6
## GO:0005198 GO:0005198 structural molecule activity     1       1/6
## GO:0005215 GO:0005215         transporter activity     0       0/6
## GO:0005488 GO:0005488                      binding     6       6/6
## GO:0009055 GO:0009055   electron transfer activity     0       0/6
##                                   geneID
## GO:0003774                              
## GO:0003824                G6PD/FASN/MSH6
## GO:0005198                           FN1
## GO:0005215                              
## GO:0005488 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0009055                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     1       1/6
## GO:0002376 GO:0002376 immune system process     4       4/6
## GO:0008152 GO:0008152     metabolic process     6       6/6
## GO:0009987 GO:0009987      cellular process     6       6/6
## GO:0016032 GO:0016032         viral process     1       1/6
## GO:0022414 GO:0022414  reproductive process     1       1/6
##                                   geneID
## GO:0000003                          MSH6
## GO:0002376            FN1/G6PD/MSH6/TFRC
## GO:0008152 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0009987 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0016032                          TFRC
## GO:0022414                          MSH6
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     3       3/6
## GO:0044423 GO:0044423           virion component     0       0/6
## GO:0110165 GO:0110165 cellular anatomical entity     6       6/6
##                                   geneID
## GO:0032991                 FN1/MSH6/TFRC
## GO:0044423                              
## GO:0110165 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/4
## GO:0003824 GO:0003824           catalytic activity     2       2/4
## GO:0005198 GO:0005198 structural molecule activity     1       1/4
## GO:0005215 GO:0005215         transporter activity     0       0/4
## GO:0005488 GO:0005488                      binding     4       4/4
## GO:0009055 GO:0009055   electron transfer activity     0       0/4
##                        geneID
## GO:0003774                   
## GO:0003824          G6PD/FASN
## GO:0005198                FN1
## GO:0005215                   
## GO:0005488 FN1/G6PD/FASN/TFRC
## GO:0009055                   
##                    ID           Description Count GeneRatio             geneID
## GO:0000003 GO:0000003          reproduction     0       0/4                   
## GO:0002376 GO:0002376 immune system process     3       3/4      FN1/G6PD/TFRC
## GO:0008152 GO:0008152     metabolic process     4       4/4 FN1/G6PD/FASN/TFRC
## GO:0009987 GO:0009987      cellular process     4       4/4 FN1/G6PD/FASN/TFRC
## GO:0016032 GO:0016032         viral process     1       1/4               TFRC
## GO:0022414 GO:0022414  reproductive process     0       0/4                   
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     2       2/4
## GO:0044423 GO:0044423           virion component     0       0/4
## GO:0110165 GO:0110165 cellular anatomical entity     4       4/4
##                        geneID
## GO:0032991           FN1/TFRC
## GO:0044423                   
## GO:0110165 FN1/G6PD/FASN/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/4
## GO:0003824 GO:0003824           catalytic activity     2       2/4
## GO:0005198 GO:0005198 structural molecule activity     1       1/4
## GO:0005215 GO:0005215         transporter activity     0       0/4
## GO:0005488 GO:0005488                      binding     4       4/4
## GO:0009055 GO:0009055   electron transfer activity     0       0/4
##                        geneID
## GO:0003774                   
## GO:0003824          G6PD/FASN
## GO:0005198                FN1
## GO:0005215                   
## GO:0005488 FN1/G6PD/FASN/TFRC
## GO:0009055                   
##                    ID           Description Count GeneRatio             geneID
## GO:0000003 GO:0000003          reproduction     0       0/4                   
## GO:0002376 GO:0002376 immune system process     3       3/4      FN1/G6PD/TFRC
## GO:0008152 GO:0008152     metabolic process     4       4/4 FN1/G6PD/FASN/TFRC
## GO:0009987 GO:0009987      cellular process     4       4/4 FN1/G6PD/FASN/TFRC
## GO:0016032 GO:0016032         viral process     1       1/4               TFRC
## GO:0022414 GO:0022414  reproductive process     0       0/4                   
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     2       2/4
## GO:0044423 GO:0044423           virion component     0       0/4
## GO:0110165 GO:0110165 cellular anatomical entity     4       4/4
##                        geneID
## GO:0032991           FN1/TFRC
## GO:0044423                   
## GO:0110165 FN1/G6PD/FASN/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/5
## GO:0003824 GO:0003824           catalytic activity     3       3/5
## GO:0005198 GO:0005198 structural molecule activity     1       1/5
## GO:0005215 GO:0005215         transporter activity     0       0/5
## GO:0005488 GO:0005488                      binding     5       5/5
## GO:0009055 GO:0009055   electron transfer activity     0       0/5
##                             geneID
## GO:0003774                        
## GO:0003824          G6PD/FASN/MSH6
## GO:0005198                     FN1
## GO:0005215                        
## GO:0005488 FN1/G6PD/FASN/MSH6/TFRC
## GO:0009055                        
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     1       1/5
## GO:0002376 GO:0002376 immune system process     4       4/5
## GO:0008152 GO:0008152     metabolic process     5       5/5
## GO:0009987 GO:0009987      cellular process     5       5/5
## GO:0016032 GO:0016032         viral process     1       1/5
## GO:0022414 GO:0022414  reproductive process     1       1/5
##                             geneID
## GO:0000003                    MSH6
## GO:0002376      FN1/G6PD/MSH6/TFRC
## GO:0008152 FN1/G6PD/FASN/MSH6/TFRC
## GO:0009987 FN1/G6PD/FASN/MSH6/TFRC
## GO:0016032                    TFRC
## GO:0022414                    MSH6
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     3       3/5
## GO:0044423 GO:0044423           virion component     0       0/5
## GO:0110165 GO:0110165 cellular anatomical entity     5       5/5
##                             geneID
## GO:0032991           FN1/MSH6/TFRC
## GO:0044423                        
## GO:0110165 FN1/G6PD/FASN/MSH6/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/6
## GO:0003824 GO:0003824           catalytic activity     3       3/6
## GO:0005198 GO:0005198 structural molecule activity     1       1/6
## GO:0005215 GO:0005215         transporter activity     0       0/6
## GO:0005488 GO:0005488                      binding     6       6/6
## GO:0009055 GO:0009055   electron transfer activity     0       0/6
##                                   geneID
## GO:0003774                              
## GO:0003824                G6PD/FASN/MSH6
## GO:0005198                           FN1
## GO:0005215                              
## GO:0005488 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0009055                              
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     1       1/6
## GO:0002376 GO:0002376 immune system process     4       4/6
## GO:0008152 GO:0008152     metabolic process     6       6/6
## GO:0009987 GO:0009987      cellular process     6       6/6
## GO:0016032 GO:0016032         viral process     1       1/6
## GO:0022414 GO:0022414  reproductive process     1       1/6
##                                   geneID
## GO:0000003                          MSH6
## GO:0002376            FN1/G6PD/MSH6/TFRC
## GO:0008152 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0009987 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
## GO:0016032                          TFRC
## GO:0022414                          MSH6
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     3       3/6
## GO:0044423 GO:0044423           virion component     0       0/6
## GO:0110165 GO:0110165 cellular anatomical entity     6       6/6
##                                   geneID
## GO:0032991                 FN1/MSH6/TFRC
## GO:0044423                              
## GO:0110165 FN1/G6PD/FASN/PDCD4/MSH6/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/4
## GO:0003824 GO:0003824           catalytic activity     2       2/4
## GO:0005198 GO:0005198 structural molecule activity     1       1/4
## GO:0005215 GO:0005215         transporter activity     0       0/4
## GO:0005488 GO:0005488                      binding     4       4/4
## GO:0009055 GO:0009055   electron transfer activity     0       0/4
##                        geneID
## GO:0003774                   
## GO:0003824          G6PD/FASN
## GO:0005198                FN1
## GO:0005215                   
## GO:0005488 FN1/G6PD/FASN/TFRC
## GO:0009055                   
##                    ID           Description Count GeneRatio             geneID
## GO:0000003 GO:0000003          reproduction     0       0/4                   
## GO:0002376 GO:0002376 immune system process     3       3/4      FN1/G6PD/TFRC
## GO:0008152 GO:0008152     metabolic process     4       4/4 FN1/G6PD/FASN/TFRC
## GO:0009987 GO:0009987      cellular process     4       4/4 FN1/G6PD/FASN/TFRC
## GO:0016032 GO:0016032         viral process     1       1/4               TFRC
## GO:0022414 GO:0022414  reproductive process     0       0/4                   
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     2       2/4
## GO:0044423 GO:0044423           virion component     0       0/4
## GO:0110165 GO:0110165 cellular anatomical entity     4       4/4
##                        geneID
## GO:0032991           FN1/TFRC
## GO:0044423                   
## GO:0110165 FN1/G6PD/FASN/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/4
## GO:0003824 GO:0003824           catalytic activity     2       2/4
## GO:0005198 GO:0005198 structural molecule activity     1       1/4
## GO:0005215 GO:0005215         transporter activity     0       0/4
## GO:0005488 GO:0005488                      binding     4       4/4
## GO:0009055 GO:0009055   electron transfer activity     0       0/4
##                        geneID
## GO:0003774                   
## GO:0003824          G6PD/FASN
## GO:0005198                FN1
## GO:0005215                   
## GO:0005488 FN1/G6PD/FASN/TFRC
## GO:0009055                   
##                    ID           Description Count GeneRatio             geneID
## GO:0000003 GO:0000003          reproduction     0       0/4                   
## GO:0002376 GO:0002376 immune system process     3       3/4      FN1/G6PD/TFRC
## GO:0008152 GO:0008152     metabolic process     4       4/4 FN1/G6PD/FASN/TFRC
## GO:0009987 GO:0009987      cellular process     4       4/4 FN1/G6PD/FASN/TFRC
## GO:0016032 GO:0016032         viral process     1       1/4               TFRC
## GO:0022414 GO:0022414  reproductive process     0       0/4                   
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     2       2/4
## GO:0044423 GO:0044423           virion component     0       0/4
## GO:0110165 GO:0110165 cellular anatomical entity     4       4/4
##                        geneID
## GO:0032991           FN1/TFRC
## GO:0044423                   
## GO:0110165 FN1/G6PD/FASN/TFRC
barplot(ggo_MF[[1]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Multigroup")

barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Onegroup")

barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 1, Multigroup")

barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 1, Multigroup")

barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Multigroup")

barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Onegroup")

barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 1, Multigroup")

barplot(ggo_MF[[8]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 1, Onegroup")

barplot(ggo_MF[[9]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Multigroup")

barplot(ggo_MF[[10]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Onegroup")

barplot(ggo_MF[[11]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 1, Multigroup")

barplot(ggo_MF[[12]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 1, Onegroup")

barplot(ggo_BP[[1]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Multigroup")

barplot(ggo_BP[[2]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Onegroup")

barplot(ggo_BP[[3]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 1, Multigroup")

barplot(ggo_BP[[4]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 1, Multigroup")

barplot(ggo_BP[[5]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Multigroup")

barplot(ggo_BP[[6]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Onegroup")

barplot(ggo_BP[[7]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 1, Multigroup")

barplot(ggo_BP[[8]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 1, Onegroup")

barplot(ggo_BP[[9]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Multigroup")

barplot(ggo_BP[[10]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Onegroup")

barplot(ggo_BP[[11]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 1, Multigroup")

barplot(ggo_BP[[12]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 1, Onegroup")

barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Multigroup")

barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Onegroup")

barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 1, Multigroup")

barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 1, Multigroup")

barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Multigroup")

barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Onegroup")

barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 1, Multigroup")

barplot(ggo_CC[[8]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 1, Onegroup")

barplot(ggo_CC[[9]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Multigroup")

barplot(ggo_CC[[10]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Onegroup")

barplot(ggo_CC[[11]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 1, Multigroup")

barplot(ggo_CC[[12]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 1, Onegroup")

B. GO Over-Representation

ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]
  ego_MF[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "MF",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_BP[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "BP",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_CC[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "CC",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
for(z in 1:length(geneNames)){
  print(head(ego_MF[[z]]))
  print(head(ego_BP[[z]]))
  print(head(ego_CC[[z]]))
}
##                    ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
##                                                                                      Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614                              oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314                                  [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315                                    3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316                           3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345                                            glucose-6-phosphate dehydrogenase activity
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue    geneID
## GO:0016616       2/5 125/18522 0.0004458624 0.002463021 0.0003906738 G6PD/FASN
## GO:0016614       2/5 135/18522 0.0005198010 0.002463021 0.0003906738 G6PD/FASN
## GO:0004314       1/5   2/18522 0.0005398402 0.002463021 0.0003906738      FASN
## GO:0004315       1/5   2/18522 0.0005398402 0.002463021 0.0003906738      FASN
## GO:0004316       1/5   2/18522 0.0005398402 0.002463021 0.0003906738      FASN
## GO:0004345       1/5   2/18522 0.0005398402 0.002463021 0.0003906738      G6PD
##            Count
## GO:0016616     2
## GO:0016614     2
## GO:0004314     1
## GO:0004315     1
## GO:0004316     1
## GO:0004345     1
##                    ID
## GO:0010039 GO:0010039
## GO:0044403 GO:0044403
## GO:0006953 GO:0006953
## GO:0002204 GO:0002204
## GO:0002208 GO:0002208
## GO:0045190 GO:0045190
##                                                                          Description
## GO:0010039                                                      response to iron ion
## GO:0044403                      biological process involved in symbiotic interaction
## GO:0006953                                                      acute-phase response
## GO:0002204 somatic recombination of immunoglobulin genes involved in immune response
## GO:0002208    somatic diversification of immunoglobulins involved in immune response
## GO:0045190                                                         isotype switching
##            GeneRatio   BgRatio       pvalue   p.adjust      qvalue
## GO:0010039       2/5  28/18888 2.113375e-05 0.00436869 0.001521082
## GO:0044403       3/5 311/18888 4.314255e-05 0.00436869 0.001521082
## GO:0006953       2/5  47/18888 6.031646e-05 0.00436869 0.001521082
## GO:0002204       2/5  53/18888 7.683924e-05 0.00436869 0.001521082
## GO:0002208       2/5  53/18888 7.683924e-05 0.00436869 0.001521082
## GO:0045190       2/5  53/18888 7.683924e-05 0.00436869 0.001521082
##                   geneID Count
## GO:0010039     G6PD/TFRC     2
## GO:0044403 FN1/FASN/TFRC     3
## GO:0006953      FN1/TFRC     2
## GO:0002204     MSH6/TFRC     2
## GO:0002208     MSH6/TFRC     2
## GO:0045190     MSH6/TFRC     2
##                    ID         Description GeneRatio   BgRatio       pvalue
## GO:0042470 GO:0042470          melanosome       2/5 112/19894 0.0003106766
## GO:0048770 GO:0048770     pigment granule       2/5 112/19894 0.0003106766
## GO:0032301 GO:0032301   MutSalpha complex       1/5   2/19894 0.0005026136
## GO:0072562 GO:0072562 blood microparticle       2/5 144/19894 0.0005129374
## GO:0042587 GO:0042587    glycogen granule       1/5   6/19894 0.0015072345
## GO:0005577 GO:0005577  fibrinogen complex       1/5   8/19894 0.0020092419
##              p.adjust      qvalue    geneID Count
## GO:0042470 0.00500114 0.002564687 FASN/TFRC     2
## GO:0048770 0.00500114 0.002564687 FASN/TFRC     2
## GO:0032301 0.00500114 0.002564687      MSH6     1
## GO:0072562 0.00500114 0.002564687  FN1/TFRC     2
## GO:0042587 0.01119435 0.005740691      FASN     1
## GO:0005577 0.01119435 0.005740691       FN1     1
##                    ID
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## GO:0004998 GO:0004998
## GO:0008659 GO:0008659
##                                                                    Description
## GO:0004314                [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315                  3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316         3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345                          glucose-6-phosphate dehydrogenase activity
## GO:0004998                                       transferrin receptor activity
## GO:0008659 (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity
##            GeneRatio BgRatio       pvalue    p.adjust       qvalue geneID Count
## GO:0004314       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   FASN     1
## GO:0004315       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   FASN     1
## GO:0004316       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   FASN     1
## GO:0004345       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   G6PD     1
## GO:0004998       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   TFRC     1
## GO:0008659       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   FASN     1
##                    ID
## GO:0010039 GO:0010039
## GO:0044403 GO:0044403
## GO:0006953 GO:0006953
## GO:0002204 GO:0002204
## GO:0002208 GO:0002208
## GO:0045190 GO:0045190
##                                                                          Description
## GO:0010039                                                      response to iron ion
## GO:0044403                      biological process involved in symbiotic interaction
## GO:0006953                                                      acute-phase response
## GO:0002204 somatic recombination of immunoglobulin genes involved in immune response
## GO:0002208    somatic diversification of immunoglobulins involved in immune response
## GO:0045190                                                         isotype switching
##            GeneRatio   BgRatio       pvalue   p.adjust      qvalue
## GO:0010039       2/6  28/18888 3.167154e-05 0.00792854 0.003156436
## GO:0044403       3/6 311/18888 8.523132e-05 0.00792854 0.003156436
## GO:0006953       2/6  47/18888 9.033104e-05 0.00792854 0.003156436
## GO:0002204       2/6  53/18888 1.150515e-04 0.00792854 0.003156436
## GO:0002208       2/6  53/18888 1.150515e-04 0.00792854 0.003156436
## GO:0045190       2/6  53/18888 1.150515e-04 0.00792854 0.003156436
##                   geneID Count
## GO:0010039     G6PD/TFRC     2
## GO:0044403 FN1/FASN/TFRC     3
## GO:0006953      FN1/TFRC     2
## GO:0002204     MSH6/TFRC     2
## GO:0002208     MSH6/TFRC     2
## GO:0045190     MSH6/TFRC     2
##                    ID         Description GeneRatio   BgRatio       pvalue
## GO:0042470 GO:0042470          melanosome       2/6 112/19894 0.0004642992
## GO:0048770 GO:0048770     pigment granule       2/6 112/19894 0.0004642992
## GO:0032301 GO:0032301   MutSalpha complex       1/6   2/19894 0.0006031211
## GO:0072562 GO:0072562 blood microparticle       2/6 144/19894 0.0007657506
## GO:0042587 GO:0042587    glycogen granule       1/6   6/19894 0.0018084541
## GO:0005577 GO:0005577  fibrinogen complex       1/6   8/19894 0.0024106661
##               p.adjust      qvalue    geneID Count
## GO:0042470 0.007466069 0.004030266 FASN/TFRC     2
## GO:0048770 0.007466069 0.004030266 FASN/TFRC     2
## GO:0032301 0.007466069 0.004030266      MSH6     1
## GO:0072562 0.007466069 0.004030266  FN1/TFRC     2
## GO:0042587 0.013430854 0.007250124      FASN     1
## GO:0005577 0.013430854 0.007250124       FN1     1
##                    ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
##                                                                                      Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614                              oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314                                  [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315                                    3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316                           3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345                                            glucose-6-phosphate dehydrogenase activity
##            GeneRatio   BgRatio       pvalue   p.adjust       qvalue    geneID
## GO:0016616       2/4 125/18522 0.0002687060 0.00141082 0.0001515382 G6PD/FASN
## GO:0016614       2/4 135/18522 0.0003133792 0.00141082 0.0001515382 G6PD/FASN
## GO:0004314       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004315       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004316       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004345       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      G6PD
##            Count
## GO:0016616     2
## GO:0016614     2
## GO:0004314     1
## GO:0004315     1
## GO:0004316     1
## GO:0004345     1
##                    ID                                              Description
## GO:0010039 GO:0010039                                     response to iron ion
## GO:0044403 GO:0044403     biological process involved in symbiotic interaction
## GO:0006953 GO:0006953                                     acute-phase response
## GO:0030099 GO:0030099                             myeloid cell differentiation
## GO:0002526 GO:0002526                              acute inflammatory response
## GO:0051702 GO:0051702 biological process involved in interaction with symbiont
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0010039       2/4  28/18888 1.269190e-05 0.003249522 0.001020648
## GO:0044403       3/4 311/18888 1.747055e-05 0.003249522 0.001020648
## GO:0006953       2/4  47/18888 3.624743e-05 0.004494682 0.001411742
## GO:0030099       3/4 439/18888 4.902361e-05 0.004559196 0.001432005
## GO:0002526       2/4 109/18888 1.965017e-04 0.013128987 0.004123706
## GO:0051702       2/4 119/18888 2.342272e-04 0.013128987 0.004123706
##                    geneID Count
## GO:0010039      G6PD/TFRC     2
## GO:0044403  FN1/FASN/TFRC     3
## GO:0006953       FN1/TFRC     2
## GO:0030099 G6PD/FASN/TFRC     3
## GO:0002526       FN1/TFRC     2
## GO:0051702       FN1/FASN     2
##                    ID                      Description GeneRatio   BgRatio
## GO:0042470 GO:0042470                       melanosome       2/4 112/19894
## GO:0048770 GO:0048770                  pigment granule       2/4 112/19894
## GO:0072562 GO:0072562              blood microparticle       2/4 144/19894
## GO:0042587 GO:0042587                 glycogen granule       1/4   6/19894
## GO:0005577 GO:0005577               fibrinogen complex       1/4   8/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex       1/4   8/19894
##                  pvalue    p.adjust      qvalue    geneID Count
## GO:0042470 0.0001870951 0.003461260 0.001477067 FASN/TFRC     2
## GO:0048770 0.0001870951 0.003461260 0.001477067 FASN/TFRC     2
## GO:0072562 0.0003092324 0.003813867 0.001627539  FN1/TFRC     2
## GO:0042587 0.0012059391 0.009914004 0.004230727      FASN     1
## GO:0005577 0.0016076763 0.009914004 0.004230727       FN1     1
## GO:1990712 0.0016076763 0.009914004 0.004230727      TFRC     1
##                    ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
##                                                                                      Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614                              oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314                                  [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315                                    3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316                           3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345                                            glucose-6-phosphate dehydrogenase activity
##            GeneRatio   BgRatio       pvalue   p.adjust       qvalue    geneID
## GO:0016616       2/4 125/18522 0.0002687060 0.00141082 0.0001515382 G6PD/FASN
## GO:0016614       2/4 135/18522 0.0003133792 0.00141082 0.0001515382 G6PD/FASN
## GO:0004314       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004315       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004316       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004345       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      G6PD
##            Count
## GO:0016616     2
## GO:0016614     2
## GO:0004314     1
## GO:0004315     1
## GO:0004316     1
## GO:0004345     1
##                    ID                                              Description
## GO:0010039 GO:0010039                                     response to iron ion
## GO:0044403 GO:0044403     biological process involved in symbiotic interaction
## GO:0006953 GO:0006953                                     acute-phase response
## GO:0030099 GO:0030099                             myeloid cell differentiation
## GO:0002526 GO:0002526                              acute inflammatory response
## GO:0051702 GO:0051702 biological process involved in interaction with symbiont
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0010039       2/4  28/18888 1.269190e-05 0.003249522 0.001020648
## GO:0044403       3/4 311/18888 1.747055e-05 0.003249522 0.001020648
## GO:0006953       2/4  47/18888 3.624743e-05 0.004494682 0.001411742
## GO:0030099       3/4 439/18888 4.902361e-05 0.004559196 0.001432005
## GO:0002526       2/4 109/18888 1.965017e-04 0.013128987 0.004123706
## GO:0051702       2/4 119/18888 2.342272e-04 0.013128987 0.004123706
##                    geneID Count
## GO:0010039      G6PD/TFRC     2
## GO:0044403  FN1/FASN/TFRC     3
## GO:0006953       FN1/TFRC     2
## GO:0030099 G6PD/FASN/TFRC     3
## GO:0002526       FN1/TFRC     2
## GO:0051702       FN1/FASN     2
##                    ID                      Description GeneRatio   BgRatio
## GO:0042470 GO:0042470                       melanosome       2/4 112/19894
## GO:0048770 GO:0048770                  pigment granule       2/4 112/19894
## GO:0072562 GO:0072562              blood microparticle       2/4 144/19894
## GO:0042587 GO:0042587                 glycogen granule       1/4   6/19894
## GO:0005577 GO:0005577               fibrinogen complex       1/4   8/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex       1/4   8/19894
##                  pvalue    p.adjust      qvalue    geneID Count
## GO:0042470 0.0001870951 0.003461260 0.001477067 FASN/TFRC     2
## GO:0048770 0.0001870951 0.003461260 0.001477067 FASN/TFRC     2
## GO:0072562 0.0003092324 0.003813867 0.001627539  FN1/TFRC     2
## GO:0042587 0.0012059391 0.009914004 0.004230727      FASN     1
## GO:0005577 0.0016076763 0.009914004 0.004230727       FN1     1
## GO:1990712 0.0016076763 0.009914004 0.004230727      TFRC     1
##                    ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
##                                                                                      Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614                              oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314                                  [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315                                    3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316                           3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345                                            glucose-6-phosphate dehydrogenase activity
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue    geneID
## GO:0016616       2/5 125/18522 0.0004458624 0.002463021 0.0003906738 G6PD/FASN
## GO:0016614       2/5 135/18522 0.0005198010 0.002463021 0.0003906738 G6PD/FASN
## GO:0004314       1/5   2/18522 0.0005398402 0.002463021 0.0003906738      FASN
## GO:0004315       1/5   2/18522 0.0005398402 0.002463021 0.0003906738      FASN
## GO:0004316       1/5   2/18522 0.0005398402 0.002463021 0.0003906738      FASN
## GO:0004345       1/5   2/18522 0.0005398402 0.002463021 0.0003906738      G6PD
##            Count
## GO:0016616     2
## GO:0016614     2
## GO:0004314     1
## GO:0004315     1
## GO:0004316     1
## GO:0004345     1
##                    ID
## GO:0010039 GO:0010039
## GO:0044403 GO:0044403
## GO:0006953 GO:0006953
## GO:0002204 GO:0002204
## GO:0002208 GO:0002208
## GO:0045190 GO:0045190
##                                                                          Description
## GO:0010039                                                      response to iron ion
## GO:0044403                      biological process involved in symbiotic interaction
## GO:0006953                                                      acute-phase response
## GO:0002204 somatic recombination of immunoglobulin genes involved in immune response
## GO:0002208    somatic diversification of immunoglobulins involved in immune response
## GO:0045190                                                         isotype switching
##            GeneRatio   BgRatio       pvalue   p.adjust      qvalue
## GO:0010039       2/5  28/18888 2.113375e-05 0.00436869 0.001521082
## GO:0044403       3/5 311/18888 4.314255e-05 0.00436869 0.001521082
## GO:0006953       2/5  47/18888 6.031646e-05 0.00436869 0.001521082
## GO:0002204       2/5  53/18888 7.683924e-05 0.00436869 0.001521082
## GO:0002208       2/5  53/18888 7.683924e-05 0.00436869 0.001521082
## GO:0045190       2/5  53/18888 7.683924e-05 0.00436869 0.001521082
##                   geneID Count
## GO:0010039     G6PD/TFRC     2
## GO:0044403 FN1/FASN/TFRC     3
## GO:0006953      FN1/TFRC     2
## GO:0002204     MSH6/TFRC     2
## GO:0002208     MSH6/TFRC     2
## GO:0045190     MSH6/TFRC     2
##                    ID         Description GeneRatio   BgRatio       pvalue
## GO:0042470 GO:0042470          melanosome       2/5 112/19894 0.0003106766
## GO:0048770 GO:0048770     pigment granule       2/5 112/19894 0.0003106766
## GO:0032301 GO:0032301   MutSalpha complex       1/5   2/19894 0.0005026136
## GO:0072562 GO:0072562 blood microparticle       2/5 144/19894 0.0005129374
## GO:0042587 GO:0042587    glycogen granule       1/5   6/19894 0.0015072345
## GO:0005577 GO:0005577  fibrinogen complex       1/5   8/19894 0.0020092419
##              p.adjust      qvalue    geneID Count
## GO:0042470 0.00500114 0.002564687 FASN/TFRC     2
## GO:0048770 0.00500114 0.002564687 FASN/TFRC     2
## GO:0032301 0.00500114 0.002564687      MSH6     1
## GO:0072562 0.00500114 0.002564687  FN1/TFRC     2
## GO:0042587 0.01119435 0.005740691      FASN     1
## GO:0005577 0.01119435 0.005740691       FN1     1
##                    ID
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## GO:0004998 GO:0004998
## GO:0008659 GO:0008659
##                                                                    Description
## GO:0004314                [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315                  3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316         3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345                          glucose-6-phosphate dehydrogenase activity
## GO:0004998                                       transferrin receptor activity
## GO:0008659 (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity
##            GeneRatio BgRatio       pvalue    p.adjust       qvalue geneID Count
## GO:0004314       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   FASN     1
## GO:0004315       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   FASN     1
## GO:0004316       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   FASN     1
## GO:0004345       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   G6PD     1
## GO:0004998       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   TFRC     1
## GO:0008659       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   FASN     1
##                    ID
## GO:0010039 GO:0010039
## GO:0044403 GO:0044403
## GO:0006953 GO:0006953
## GO:0002204 GO:0002204
## GO:0002208 GO:0002208
## GO:0045190 GO:0045190
##                                                                          Description
## GO:0010039                                                      response to iron ion
## GO:0044403                      biological process involved in symbiotic interaction
## GO:0006953                                                      acute-phase response
## GO:0002204 somatic recombination of immunoglobulin genes involved in immune response
## GO:0002208    somatic diversification of immunoglobulins involved in immune response
## GO:0045190                                                         isotype switching
##            GeneRatio   BgRatio       pvalue   p.adjust      qvalue
## GO:0010039       2/6  28/18888 3.167154e-05 0.00792854 0.003156436
## GO:0044403       3/6 311/18888 8.523132e-05 0.00792854 0.003156436
## GO:0006953       2/6  47/18888 9.033104e-05 0.00792854 0.003156436
## GO:0002204       2/6  53/18888 1.150515e-04 0.00792854 0.003156436
## GO:0002208       2/6  53/18888 1.150515e-04 0.00792854 0.003156436
## GO:0045190       2/6  53/18888 1.150515e-04 0.00792854 0.003156436
##                   geneID Count
## GO:0010039     G6PD/TFRC     2
## GO:0044403 FN1/FASN/TFRC     3
## GO:0006953      FN1/TFRC     2
## GO:0002204     MSH6/TFRC     2
## GO:0002208     MSH6/TFRC     2
## GO:0045190     MSH6/TFRC     2
##                    ID         Description GeneRatio   BgRatio       pvalue
## GO:0042470 GO:0042470          melanosome       2/6 112/19894 0.0004642992
## GO:0048770 GO:0048770     pigment granule       2/6 112/19894 0.0004642992
## GO:0032301 GO:0032301   MutSalpha complex       1/6   2/19894 0.0006031211
## GO:0072562 GO:0072562 blood microparticle       2/6 144/19894 0.0007657506
## GO:0042587 GO:0042587    glycogen granule       1/6   6/19894 0.0018084541
## GO:0005577 GO:0005577  fibrinogen complex       1/6   8/19894 0.0024106661
##               p.adjust      qvalue    geneID Count
## GO:0042470 0.007466069 0.004030266 FASN/TFRC     2
## GO:0048770 0.007466069 0.004030266 FASN/TFRC     2
## GO:0032301 0.007466069 0.004030266      MSH6     1
## GO:0072562 0.007466069 0.004030266  FN1/TFRC     2
## GO:0042587 0.013430854 0.007250124      FASN     1
## GO:0005577 0.013430854 0.007250124       FN1     1
##                    ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
##                                                                                      Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614                              oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314                                  [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315                                    3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316                           3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345                                            glucose-6-phosphate dehydrogenase activity
##            GeneRatio   BgRatio       pvalue   p.adjust       qvalue    geneID
## GO:0016616       2/4 125/18522 0.0002687060 0.00141082 0.0001515382 G6PD/FASN
## GO:0016614       2/4 135/18522 0.0003133792 0.00141082 0.0001515382 G6PD/FASN
## GO:0004314       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004315       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004316       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004345       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      G6PD
##            Count
## GO:0016616     2
## GO:0016614     2
## GO:0004314     1
## GO:0004315     1
## GO:0004316     1
## GO:0004345     1
##                    ID                                              Description
## GO:0010039 GO:0010039                                     response to iron ion
## GO:0044403 GO:0044403     biological process involved in symbiotic interaction
## GO:0006953 GO:0006953                                     acute-phase response
## GO:0030099 GO:0030099                             myeloid cell differentiation
## GO:0002526 GO:0002526                              acute inflammatory response
## GO:0051702 GO:0051702 biological process involved in interaction with symbiont
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0010039       2/4  28/18888 1.269190e-05 0.003249522 0.001020648
## GO:0044403       3/4 311/18888 1.747055e-05 0.003249522 0.001020648
## GO:0006953       2/4  47/18888 3.624743e-05 0.004494682 0.001411742
## GO:0030099       3/4 439/18888 4.902361e-05 0.004559196 0.001432005
## GO:0002526       2/4 109/18888 1.965017e-04 0.013128987 0.004123706
## GO:0051702       2/4 119/18888 2.342272e-04 0.013128987 0.004123706
##                    geneID Count
## GO:0010039      G6PD/TFRC     2
## GO:0044403  FN1/FASN/TFRC     3
## GO:0006953       FN1/TFRC     2
## GO:0030099 G6PD/FASN/TFRC     3
## GO:0002526       FN1/TFRC     2
## GO:0051702       FN1/FASN     2
##                    ID                      Description GeneRatio   BgRatio
## GO:0042470 GO:0042470                       melanosome       2/4 112/19894
## GO:0048770 GO:0048770                  pigment granule       2/4 112/19894
## GO:0072562 GO:0072562              blood microparticle       2/4 144/19894
## GO:0042587 GO:0042587                 glycogen granule       1/4   6/19894
## GO:0005577 GO:0005577               fibrinogen complex       1/4   8/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex       1/4   8/19894
##                  pvalue    p.adjust      qvalue    geneID Count
## GO:0042470 0.0001870951 0.003461260 0.001477067 FASN/TFRC     2
## GO:0048770 0.0001870951 0.003461260 0.001477067 FASN/TFRC     2
## GO:0072562 0.0003092324 0.003813867 0.001627539  FN1/TFRC     2
## GO:0042587 0.0012059391 0.009914004 0.004230727      FASN     1
## GO:0005577 0.0016076763 0.009914004 0.004230727       FN1     1
## GO:1990712 0.0016076763 0.009914004 0.004230727      TFRC     1
##                    ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
##                                                                                      Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614                              oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314                                  [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315                                    3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316                           3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345                                            glucose-6-phosphate dehydrogenase activity
##            GeneRatio   BgRatio       pvalue   p.adjust       qvalue    geneID
## GO:0016616       2/4 125/18522 0.0002687060 0.00141082 0.0001515382 G6PD/FASN
## GO:0016614       2/4 135/18522 0.0003133792 0.00141082 0.0001515382 G6PD/FASN
## GO:0004314       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004315       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004316       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004345       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      G6PD
##            Count
## GO:0016616     2
## GO:0016614     2
## GO:0004314     1
## GO:0004315     1
## GO:0004316     1
## GO:0004345     1
##                    ID                                              Description
## GO:0010039 GO:0010039                                     response to iron ion
## GO:0044403 GO:0044403     biological process involved in symbiotic interaction
## GO:0006953 GO:0006953                                     acute-phase response
## GO:0030099 GO:0030099                             myeloid cell differentiation
## GO:0002526 GO:0002526                              acute inflammatory response
## GO:0051702 GO:0051702 biological process involved in interaction with symbiont
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0010039       2/4  28/18888 1.269190e-05 0.003249522 0.001020648
## GO:0044403       3/4 311/18888 1.747055e-05 0.003249522 0.001020648
## GO:0006953       2/4  47/18888 3.624743e-05 0.004494682 0.001411742
## GO:0030099       3/4 439/18888 4.902361e-05 0.004559196 0.001432005
## GO:0002526       2/4 109/18888 1.965017e-04 0.013128987 0.004123706
## GO:0051702       2/4 119/18888 2.342272e-04 0.013128987 0.004123706
##                    geneID Count
## GO:0010039      G6PD/TFRC     2
## GO:0044403  FN1/FASN/TFRC     3
## GO:0006953       FN1/TFRC     2
## GO:0030099 G6PD/FASN/TFRC     3
## GO:0002526       FN1/TFRC     2
## GO:0051702       FN1/FASN     2
##                    ID                      Description GeneRatio   BgRatio
## GO:0042470 GO:0042470                       melanosome       2/4 112/19894
## GO:0048770 GO:0048770                  pigment granule       2/4 112/19894
## GO:0072562 GO:0072562              blood microparticle       2/4 144/19894
## GO:0042587 GO:0042587                 glycogen granule       1/4   6/19894
## GO:0005577 GO:0005577               fibrinogen complex       1/4   8/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex       1/4   8/19894
##                  pvalue    p.adjust      qvalue    geneID Count
## GO:0042470 0.0001870951 0.003461260 0.001477067 FASN/TFRC     2
## GO:0048770 0.0001870951 0.003461260 0.001477067 FASN/TFRC     2
## GO:0072562 0.0003092324 0.003813867 0.001627539  FN1/TFRC     2
## GO:0042587 0.0012059391 0.009914004 0.004230727      FASN     1
## GO:0005577 0.0016076763 0.009914004 0.004230727       FN1     1
## GO:1990712 0.0016076763 0.009914004 0.004230727      TFRC     1
##                    ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
##                                                                                      Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614                              oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314                                  [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315                                    3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316                           3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345                                            glucose-6-phosphate dehydrogenase activity
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue    geneID
## GO:0016616       2/5 125/18522 0.0004458624 0.002463021 0.0003906738 G6PD/FASN
## GO:0016614       2/5 135/18522 0.0005198010 0.002463021 0.0003906738 G6PD/FASN
## GO:0004314       1/5   2/18522 0.0005398402 0.002463021 0.0003906738      FASN
## GO:0004315       1/5   2/18522 0.0005398402 0.002463021 0.0003906738      FASN
## GO:0004316       1/5   2/18522 0.0005398402 0.002463021 0.0003906738      FASN
## GO:0004345       1/5   2/18522 0.0005398402 0.002463021 0.0003906738      G6PD
##            Count
## GO:0016616     2
## GO:0016614     2
## GO:0004314     1
## GO:0004315     1
## GO:0004316     1
## GO:0004345     1
##                    ID
## GO:0010039 GO:0010039
## GO:0044403 GO:0044403
## GO:0006953 GO:0006953
## GO:0002204 GO:0002204
## GO:0002208 GO:0002208
## GO:0045190 GO:0045190
##                                                                          Description
## GO:0010039                                                      response to iron ion
## GO:0044403                      biological process involved in symbiotic interaction
## GO:0006953                                                      acute-phase response
## GO:0002204 somatic recombination of immunoglobulin genes involved in immune response
## GO:0002208    somatic diversification of immunoglobulins involved in immune response
## GO:0045190                                                         isotype switching
##            GeneRatio   BgRatio       pvalue   p.adjust      qvalue
## GO:0010039       2/5  28/18888 2.113375e-05 0.00436869 0.001521082
## GO:0044403       3/5 311/18888 4.314255e-05 0.00436869 0.001521082
## GO:0006953       2/5  47/18888 6.031646e-05 0.00436869 0.001521082
## GO:0002204       2/5  53/18888 7.683924e-05 0.00436869 0.001521082
## GO:0002208       2/5  53/18888 7.683924e-05 0.00436869 0.001521082
## GO:0045190       2/5  53/18888 7.683924e-05 0.00436869 0.001521082
##                   geneID Count
## GO:0010039     G6PD/TFRC     2
## GO:0044403 FN1/FASN/TFRC     3
## GO:0006953      FN1/TFRC     2
## GO:0002204     MSH6/TFRC     2
## GO:0002208     MSH6/TFRC     2
## GO:0045190     MSH6/TFRC     2
##                    ID         Description GeneRatio   BgRatio       pvalue
## GO:0042470 GO:0042470          melanosome       2/5 112/19894 0.0003106766
## GO:0048770 GO:0048770     pigment granule       2/5 112/19894 0.0003106766
## GO:0032301 GO:0032301   MutSalpha complex       1/5   2/19894 0.0005026136
## GO:0072562 GO:0072562 blood microparticle       2/5 144/19894 0.0005129374
## GO:0042587 GO:0042587    glycogen granule       1/5   6/19894 0.0015072345
## GO:0005577 GO:0005577  fibrinogen complex       1/5   8/19894 0.0020092419
##              p.adjust      qvalue    geneID Count
## GO:0042470 0.00500114 0.002564687 FASN/TFRC     2
## GO:0048770 0.00500114 0.002564687 FASN/TFRC     2
## GO:0032301 0.00500114 0.002564687      MSH6     1
## GO:0072562 0.00500114 0.002564687  FN1/TFRC     2
## GO:0042587 0.01119435 0.005740691      FASN     1
## GO:0005577 0.01119435 0.005740691       FN1     1
##                    ID
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
## GO:0004998 GO:0004998
## GO:0008659 GO:0008659
##                                                                    Description
## GO:0004314                [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315                  3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316         3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345                          glucose-6-phosphate dehydrogenase activity
## GO:0004998                                       transferrin receptor activity
## GO:0008659 (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity
##            GeneRatio BgRatio       pvalue    p.adjust       qvalue geneID Count
## GO:0004314       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   FASN     1
## GO:0004315       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   FASN     1
## GO:0004316       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   FASN     1
## GO:0004345       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   G6PD     1
## GO:0004998       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   TFRC     1
## GO:0008659       1/6 2/18522 0.0006477907 0.003240407 0.0006541557   FASN     1
##                    ID
## GO:0010039 GO:0010039
## GO:0044403 GO:0044403
## GO:0006953 GO:0006953
## GO:0002204 GO:0002204
## GO:0002208 GO:0002208
## GO:0045190 GO:0045190
##                                                                          Description
## GO:0010039                                                      response to iron ion
## GO:0044403                      biological process involved in symbiotic interaction
## GO:0006953                                                      acute-phase response
## GO:0002204 somatic recombination of immunoglobulin genes involved in immune response
## GO:0002208    somatic diversification of immunoglobulins involved in immune response
## GO:0045190                                                         isotype switching
##            GeneRatio   BgRatio       pvalue   p.adjust      qvalue
## GO:0010039       2/6  28/18888 3.167154e-05 0.00792854 0.003156436
## GO:0044403       3/6 311/18888 8.523132e-05 0.00792854 0.003156436
## GO:0006953       2/6  47/18888 9.033104e-05 0.00792854 0.003156436
## GO:0002204       2/6  53/18888 1.150515e-04 0.00792854 0.003156436
## GO:0002208       2/6  53/18888 1.150515e-04 0.00792854 0.003156436
## GO:0045190       2/6  53/18888 1.150515e-04 0.00792854 0.003156436
##                   geneID Count
## GO:0010039     G6PD/TFRC     2
## GO:0044403 FN1/FASN/TFRC     3
## GO:0006953      FN1/TFRC     2
## GO:0002204     MSH6/TFRC     2
## GO:0002208     MSH6/TFRC     2
## GO:0045190     MSH6/TFRC     2
##                    ID         Description GeneRatio   BgRatio       pvalue
## GO:0042470 GO:0042470          melanosome       2/6 112/19894 0.0004642992
## GO:0048770 GO:0048770     pigment granule       2/6 112/19894 0.0004642992
## GO:0032301 GO:0032301   MutSalpha complex       1/6   2/19894 0.0006031211
## GO:0072562 GO:0072562 blood microparticle       2/6 144/19894 0.0007657506
## GO:0042587 GO:0042587    glycogen granule       1/6   6/19894 0.0018084541
## GO:0005577 GO:0005577  fibrinogen complex       1/6   8/19894 0.0024106661
##               p.adjust      qvalue    geneID Count
## GO:0042470 0.007466069 0.004030266 FASN/TFRC     2
## GO:0048770 0.007466069 0.004030266 FASN/TFRC     2
## GO:0032301 0.007466069 0.004030266      MSH6     1
## GO:0072562 0.007466069 0.004030266  FN1/TFRC     2
## GO:0042587 0.013430854 0.007250124      FASN     1
## GO:0005577 0.013430854 0.007250124       FN1     1
##                    ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
##                                                                                      Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614                              oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314                                  [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315                                    3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316                           3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345                                            glucose-6-phosphate dehydrogenase activity
##            GeneRatio   BgRatio       pvalue   p.adjust       qvalue    geneID
## GO:0016616       2/4 125/18522 0.0002687060 0.00141082 0.0001515382 G6PD/FASN
## GO:0016614       2/4 135/18522 0.0003133792 0.00141082 0.0001515382 G6PD/FASN
## GO:0004314       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004315       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004316       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004345       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      G6PD
##            Count
## GO:0016616     2
## GO:0016614     2
## GO:0004314     1
## GO:0004315     1
## GO:0004316     1
## GO:0004345     1
##                    ID                                              Description
## GO:0010039 GO:0010039                                     response to iron ion
## GO:0044403 GO:0044403     biological process involved in symbiotic interaction
## GO:0006953 GO:0006953                                     acute-phase response
## GO:0030099 GO:0030099                             myeloid cell differentiation
## GO:0002526 GO:0002526                              acute inflammatory response
## GO:0051702 GO:0051702 biological process involved in interaction with symbiont
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0010039       2/4  28/18888 1.269190e-05 0.003249522 0.001020648
## GO:0044403       3/4 311/18888 1.747055e-05 0.003249522 0.001020648
## GO:0006953       2/4  47/18888 3.624743e-05 0.004494682 0.001411742
## GO:0030099       3/4 439/18888 4.902361e-05 0.004559196 0.001432005
## GO:0002526       2/4 109/18888 1.965017e-04 0.013128987 0.004123706
## GO:0051702       2/4 119/18888 2.342272e-04 0.013128987 0.004123706
##                    geneID Count
## GO:0010039      G6PD/TFRC     2
## GO:0044403  FN1/FASN/TFRC     3
## GO:0006953       FN1/TFRC     2
## GO:0030099 G6PD/FASN/TFRC     3
## GO:0002526       FN1/TFRC     2
## GO:0051702       FN1/FASN     2
##                    ID                      Description GeneRatio   BgRatio
## GO:0042470 GO:0042470                       melanosome       2/4 112/19894
## GO:0048770 GO:0048770                  pigment granule       2/4 112/19894
## GO:0072562 GO:0072562              blood microparticle       2/4 144/19894
## GO:0042587 GO:0042587                 glycogen granule       1/4   6/19894
## GO:0005577 GO:0005577               fibrinogen complex       1/4   8/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex       1/4   8/19894
##                  pvalue    p.adjust      qvalue    geneID Count
## GO:0042470 0.0001870951 0.003461260 0.001477067 FASN/TFRC     2
## GO:0048770 0.0001870951 0.003461260 0.001477067 FASN/TFRC     2
## GO:0072562 0.0003092324 0.003813867 0.001627539  FN1/TFRC     2
## GO:0042587 0.0012059391 0.009914004 0.004230727      FASN     1
## GO:0005577 0.0016076763 0.009914004 0.004230727       FN1     1
## GO:1990712 0.0016076763 0.009914004 0.004230727      TFRC     1
##                    ID
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## GO:0004314 GO:0004314
## GO:0004315 GO:0004315
## GO:0004316 GO:0004316
## GO:0004345 GO:0004345
##                                                                                      Description
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614                              oxidoreductase activity, acting on CH-OH group of donors
## GO:0004314                                  [acyl-carrier-protein] S-malonyltransferase activity
## GO:0004315                                    3-oxoacyl-[acyl-carrier-protein] synthase activity
## GO:0004316                           3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
## GO:0004345                                            glucose-6-phosphate dehydrogenase activity
##            GeneRatio   BgRatio       pvalue   p.adjust       qvalue    geneID
## GO:0016616       2/4 125/18522 0.0002687060 0.00141082 0.0001515382 G6PD/FASN
## GO:0016614       2/4 135/18522 0.0003133792 0.00141082 0.0001515382 G6PD/FASN
## GO:0004314       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004315       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004316       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      FASN
## GO:0004345       1/4   2/18522 0.0004318838 0.00141082 0.0001515382      G6PD
##            Count
## GO:0016616     2
## GO:0016614     2
## GO:0004314     1
## GO:0004315     1
## GO:0004316     1
## GO:0004345     1
##                    ID                                              Description
## GO:0010039 GO:0010039                                     response to iron ion
## GO:0044403 GO:0044403     biological process involved in symbiotic interaction
## GO:0006953 GO:0006953                                     acute-phase response
## GO:0030099 GO:0030099                             myeloid cell differentiation
## GO:0002526 GO:0002526                              acute inflammatory response
## GO:0051702 GO:0051702 biological process involved in interaction with symbiont
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0010039       2/4  28/18888 1.269190e-05 0.003249522 0.001020648
## GO:0044403       3/4 311/18888 1.747055e-05 0.003249522 0.001020648
## GO:0006953       2/4  47/18888 3.624743e-05 0.004494682 0.001411742
## GO:0030099       3/4 439/18888 4.902361e-05 0.004559196 0.001432005
## GO:0002526       2/4 109/18888 1.965017e-04 0.013128987 0.004123706
## GO:0051702       2/4 119/18888 2.342272e-04 0.013128987 0.004123706
##                    geneID Count
## GO:0010039      G6PD/TFRC     2
## GO:0044403  FN1/FASN/TFRC     3
## GO:0006953       FN1/TFRC     2
## GO:0030099 G6PD/FASN/TFRC     3
## GO:0002526       FN1/TFRC     2
## GO:0051702       FN1/FASN     2
##                    ID                      Description GeneRatio   BgRatio
## GO:0042470 GO:0042470                       melanosome       2/4 112/19894
## GO:0048770 GO:0048770                  pigment granule       2/4 112/19894
## GO:0072562 GO:0072562              blood microparticle       2/4 144/19894
## GO:0042587 GO:0042587                 glycogen granule       1/4   6/19894
## GO:0005577 GO:0005577               fibrinogen complex       1/4   8/19894
## GO:1990712 GO:1990712 HFE-transferrin receptor complex       1/4   8/19894
##                  pvalue    p.adjust      qvalue    geneID Count
## GO:0042470 0.0001870951 0.003461260 0.001477067 FASN/TFRC     2
## GO:0048770 0.0001870951 0.003461260 0.001477067 FASN/TFRC     2
## GO:0072562 0.0003092324 0.003813867 0.001627539  FN1/TFRC     2
## GO:0042587 0.0012059391 0.009914004 0.004230727      FASN     1
## GO:0005577 0.0016076763 0.009914004 0.004230727       FN1     1
## GO:1990712 0.0016076763 0.009914004 0.004230727      TFRC     1
barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Multigroup")

barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Onegroup")

barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Multigroup")

barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Multigroup")

barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Multigroup")

barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Onegroup")

barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Multigroup")

barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Onegroup")

barplot(ego_MF[[9]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Multigroup")

barplot(ego_MF[[10]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Onegroup")

barplot(ego_MF[[11]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Multigroup")

barplot(ego_MF[[12]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Onegroup")

barplot(ego_BP[[1]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Multigroup")

barplot(ego_BP[[2]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Onegroup")

barplot(ego_BP[[3]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Multigroup")

barplot(ego_BP[[4]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Multigroup")

barplot(ego_BP[[5]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Multigroup")

barplot(ego_BP[[6]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Onegroup")

barplot(ego_BP[[7]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Multigroup")

barplot(ego_BP[[8]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Onegroup")

barplot(ego_BP[[9]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Multigroup")

barplot(ego_BP[[10]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Onegroup")

barplot(ego_BP[[11]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Multigroup")

barplot(ego_BP[[12]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Onegroup")

barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Multigroup")

barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Onegroup")

barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Multigroup")

barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Multigroup")

barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Multigroup")

barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Onegroup")

barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Multigroup")

barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Onegroup")

barplot(ego_CC[[9]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Multigroup")

barplot(ego_CC[[10]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Onegroup")

barplot(ego_CC[[11]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Multigroup")

barplot(ego_CC[[12]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Onegroup")

DAG plots for ego

goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Multigroup")

goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Onegroup")

goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Multigroup")

goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Multigroup")

goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Multigroup")

goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Onegroup")

goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Multigroup")

goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Onegroup")

goplot(ego_MF[[9]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Multigroup")

goplot(ego_MF[[10]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Onegroup")

goplot(ego_MF[[11]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Multigroup")

goplot(ego_MF[[12]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Onegroup")

goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Multigroup")
## Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Onegroup")

goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Multigroup")

goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Multigroup")

goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Multigroup")
## Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Onegroup")

goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Multigroup")

goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Onegroup")

goplot(ego_BP[[9]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Multigroup")
## Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[10]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Onegroup")

goplot(ego_BP[[11]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Multigroup")

goplot(ego_BP[[12]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Onegroup")

goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Multigroup")

goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Onegroup")

goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Multigroup")

goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Multigroup")

goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Multigroup")

goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Onegroup")

goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Multigroup")

goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Onegroup")

goplot(ego_CC[[9]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Multigroup")

goplot(ego_CC[[10]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Onegroup")

goplot(ego_CC[[11]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Multigroup")

goplot(ego_CC[[12]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Onegroup")

3. Export Pathway Analysis result to data

pathway = list("ggo_MF" = ggo_MF,
               "ggo_BP" = ggo_BP,
               "ggo_CC" = ggo_CC,
               "ego_MF" = ego_MF,
               "ego_BP" = ego_BP,
               "ego_CC" = ego_CC)

saveRDS(pathway, file = "data/out_pathway/pathways_squeezy.rds")